On the left is a floating table of contents for navigating between major sections of output:
Within each major section, content is split into tabs that are spread horizontally across the screen. By default, the About tab for each section is showing. Click on any tab to see specifics.
This section contains tables and graphs, in separate tabs.
To detect errors in data sets, the information in this section should be reviewed by Reserve data practitioners. These results are meant to help you find issues that need to be corrected in the raw data, and decide whether plots or data should be removed from analyses (e.g., “off season” surveys, plots no longer monitored, restoration sites).
There were 1 rows with no data. These rows were removed from the dataset before further processing. If rows were removed, relevant information is in a table below.
If monitoring plots did not have data in at least 3 separate years, they were removed from the dataset before statistical analyses. These plots do appear in the plots and information in the Exploration/QAQC and Summary Bar Chart sections of this document, but were removed before Univariate and Multivariate analyses.
In this dataset, there were 1 such plots removed. If plots were removed, relevant information is in a table below.
There were 0 data points that were removed due to QA/QC flags. If data points were removed, relevant information is in a table below.
| Site | 2010 | 2011 | 2013 | 2014 | 2016 | 2017 | 2018 | 2019 | 2020 | 2021 | 2022 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| BC | 29 | 30 | 30 | 30 | 30 | 30 | 30 | 30 | 30 | 30 | 30 |
| GBF | 39 | 39 | 39 | 39 | 39 | 39 | 39 | 39 | 39 | 39 | 39 |
| SP | 43 | 44 | 44 | 45 | 45 | 45 | 45 | 45 | 45 | 45 | 45 |
| Vegetation_Zone | 2010 | 2011 | 2013 | 2014 | 2016 | 2017 | 2018 | 2019 | 2020 | 2021 | 2022 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| L-Low Marsh | 21 | 22 | 22 | 22 | 22 | 22 | 22 | 22 | 22 | 22 | 22 |
| T-Transition | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 |
| H-High Marsh | 42 | 42 | 42 | 42 | 42 | 42 | 42 | 42 | 42 | 42 | 42 |
| UE-Upland Edge | 16 | 17 | 17 | 18 | 18 | 18 | 18 | 18 | 18 | 18 | 18 |
Make sure the colors below correctly represent which Vegetation Zones your plots belong to. If something looks wrong, it needs to be corrected in the ‘Station_Table’ tab of your data workbook.
EMI, Ecotone Migration Index, is the proportional cover of species/covers or species/cover groupings that are expected to increase within a vegetation zone as sea level rises. These species were identified by reserve staff, for each zone, in the ‘veg-specs.xlsx’ file.
Species considered to be ‘migrators’ within each zone are denoted by ‘x’ in the following table:
| Species | L-Low Marsh | T-Transition | H-High Marsh | UE-Upland Edge |
|---|---|---|---|---|
| Algae | X | X | X | X |
| Ascophyllum nodosum | X | X | X | X |
| Ascophyllum nodosum var. scorpioides | X | X | X | X |
| Bare | X | X | X | X |
| Fucus spiralis | X | X | X | X |
| Fucus spp. | X | X | X | X |
| Fucus vesiculosus | X | X | X | X |
| Gracilaria spp. | X | X | X | X |
| Ulva lactuca | X | X | X | X |
| Ulva spp. | X | X | X | X |
| Vaucheria spp. | X | X | X | X |
| Water | X | X | X | X |
| Spartina alterniflora | X | X | X | |
| Agalinis maritima | X | |||
| Agrostis stolonifera | X | |||
| Amaranthus cannabinus | X | |||
| Ammophila breviligulata | X | |||
| Anthoxanthum nitens | X | |||
| Asparagus officinalis | X | |||
| Atriplex patula | X | |||
| Baccharis halimifolia | X | |||
| Bolboschoenus maritimus | X | |||
| Bolboschoenus robustus | X | |||
| Calystegia sepium | X | |||
| Carex hormathodes | X | |||
| Carex paleacea | X | |||
| Cuscuta gronovii | X | |||
| Cuscuta spp. | X | |||
| Distichlis spicata | X | |||
| Eleocharis parvula | X | |||
| Elymus virginicus | X | |||
| Euthamia graminifolia | X | |||
| Festuca rubra | X | |||
| Galium lanceolatum | X | |||
| Galium palustre | X | |||
| Hibiscus moscheutos | X | |||
| Hordeum spp. | X | |||
| Iva frutescens | X | |||
| Juncus articulatus | X | |||
| Juncus balticus | X | |||
| Juncus gerardii | X | |||
| Juncus spp. | X | |||
| Limonium carolinianum | X | |||
| Lysimachia maritima | X | |||
| Lythrum salicaria | X | |||
| Myrica gale | X | |||
| Panicum virgatum | X | |||
| Phragmites australis | X | |||
| Phragmites australis ssp. americanus | X | |||
| Plantago maritima | X | |||
| Pluchea odorata | X | |||
| Polygonum ramosissimum | X | |||
| Potentilla anserina | X | |||
| Prunus maritima | X | |||
| Puccinellia maritima | X | |||
| Rosa multiflora | X | |||
| Rosa rugosa | X | |||
| Ruppia maritima | X | |||
| Salicornia depressa | X | |||
| Salicornia maritima | X | |||
| Salicornia spp. | X | |||
| Schoenoplectus americanus | X | |||
| Schoenoplectus pungens | X | |||
| Schoenoplectus spp. | X | |||
| Scirpus cyperinus | X | |||
| Setaria spp. | X | |||
| Solidago sempervirens | X | |||
| Spartina X caespitosa | X | |||
| Spartina alterniflora (short) | X | |||
| Spartina patens | X | |||
| Spartina patens hybrid | X | |||
| Spartina pectinata | X | |||
| Spergularia salina | X | |||
| Suaeda linearis | X | |||
| Suaeda maritima | X | |||
| Symphyotrichum subulatum | X | |||
| Symphyotrichum tenuifolium | X | |||
| Thinopyrum pungens | X | |||
| Toxicodendron radicans | X | |||
| Triglochin maritima | X | |||
| Typha angustifolia | X |
This section contains summary graphics. The color palettes are
generated via the khroma R package and were developed to be
colorblind-friendly.
These summary figures tell a graphical story about current conditions and trends through time. There are two types of figure:
The species/groups identified by the Reserve for these graphs are (in order):
And so the groups appearing in the plots should be (alphabetically):
These were automatically calculated as the species having the highest mean cover, across all plots and dates.
One spatial graph was generated for each Site. This can be changed between the options of Site and Transect in the “More_Options” sheet of the “veg-specs.xlsx” file.
Each panel on the graphs represents an individual vegetation plot, showing 4 evenly spaced-through-time samples, of the species choices from the “Analysis_Specs” sheet of the “veg-specs.xlsx” file.
Plots without associated spatial locations will not be included in these graphics.
A tab will be generated for results of each response variable. The response variables consist of each of the (up to) 4 response variables identified in the Analysis Specs spreadsheet, (up to) 2 custom metrics identified in the Analysis Specs spreadsheet, EMI (Ecotone Migration Index), Species Richness, and Shannon-Weiner Diversity Index. You will see the same tables and graphics for each.
The main statistical model used is a linear mixed model, via
lme4::lmer(), with the form
y ~ Vegetation Zone + Time + Zone*Time + 1|Plot, where
y is the response variable given in the tab, and each
individual plot has a random intercept.
If only one vegetation zone is present in the data file, Vegetation
Zone is removed and the statistical model is simplified to
y ~ Time + 1|Plot.
The reserve-identified univariate response variables are:
Any custom metrics specified in the ‘Analysis_Specs’ sheet of the ‘veg-specs.xlsx’ file are calculated here, for inclusion in univariate analyses.
If you do not see a tab for a metric you believe you defined, look just below these bullet points to see if there are error messages showing up in little boxes that are different from other text - these may be helpful in troubleshooting. There are a few likely reasons for problems:
## Created new column: A-Algae
EMI, Ecotone Migration Index, is the proportional cover of species/covers or species/cover groupings that are expected to increase within a vegetation zone as sea level rises. These species were identified by reserve staff, for each zone, in the ‘veg-specs.xlsx’ file.
See the ‘EMI’ tab in the ‘Exploratory and QA/QC’ section of this document for a table of species considered to be ‘ecotone migrators’ for each zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 2.5850 | 2.5850 | 1 | 1130.02 | 88.17 | 0.0000 |
| Vegetation_Zone | 2.7803 | 0.9268 | 3 | 155.09 | 31.61 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 0.2823 | 0.0941 | 3 | 1129.83 | 3.21 | 0.0224 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0133 | 0.0029 | 0.008 | 0.019 | 4.6 | 1129.9 | 0.0000 |
| T-Transition | 0.0184 | 0.0024 | 0.014 | 0.023 | 7.8 | 1129.0 | 0.0000 |
| H-High Marsh | 0.0092 | 0.0021 | 0.005 | 0.013 | 4.4 | 1129.0 | 0.0000 |
| UE-Upland Edge | 0.0096 | 0.0032 | 0.003 | 0.016 | 3.0 | 1131.1 | 0.0032 |
| R2m | R2c |
|---|---|
| 0.439 | 0.755 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
Species Richness, calculated on all non-abiotic, non-dead, and
non-overstory columns; using the vegan package.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 32.884 | 32.8840 | 1 | 1129.82 | 22.17 | 0.0000 |
| Vegetation_Zone | 140.197 | 46.7323 | 3 | 145.33 | 31.50 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 30.113 | 10.0377 | 3 | 1129.67 | 6.77 | 0.0002 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0133 | 0.0207 | -0.027 | 0.054 | 0.6 | 1129.7 | 0.5217 |
| T-Transition | -0.0861 | 0.0168 | -0.119 | -0.053 | -5.1 | 1129.0 | 0.0000 |
| H-High Marsh | -0.0193 | 0.0147 | -0.048 | 0.010 | -1.3 | 1129.0 | 0.1894 |
| UE-Upland Edge | -0.0878 | 0.0231 | -0.133 | -0.043 | -3.8 | 1130.7 | 0.0001 |
| R2m | R2c |
|---|---|
| 0.347 | 0.754 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
Shannon-Weiner Diversity index, calculated on all non-abiotic,
non-dead, and non-overstory columns; using the vegan
package.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 2.0755 | 2.0755 | 1 | 1129.81 | 26.69 | 0 |
| Vegetation_Zone | 5.5518 | 1.8506 | 3 | 144.83 | 23.79 | 0 |
| Years_sinceStart:Vegetation_Zone | 2.5077 | 0.8359 | 3 | 1129.66 | 10.75 | 0 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0032 | 0.0047 | -0.006 | 0.013 | 0.7 | 1129.7 | 0.4951 |
| T-Transition | -0.0277 | 0.0039 | -0.035 | -0.020 | -7.2 | 1129.0 | 0.0000 |
| H-High Marsh | -0.0046 | 0.0034 | -0.011 | 0.002 | -1.4 | 1129.0 | 0.1732 |
| UE-Upland Edge | -0.0162 | 0.0053 | -0.027 | -0.006 | -3.1 | 1130.6 | 0.0022 |
| R2m | R2c |
|---|---|
| 0.3 | 0.739 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 1629.731 | 1629.731 | 1 | 1130.31 | 5.04 | 0.0249 |
| Vegetation_Zone | 4720.645 | 1573.549 | 3 | 169.57 | 4.87 | 0.0028 |
| Years_sinceStart:Vegetation_Zone | 3405.042 | 1135.014 | 3 | 1130.06 | 3.51 | 0.0148 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 1.0755 | 0.3055 | 0.476 | 1.675 | 3.5 | 1130.2 | 0.0004 |
| T-Transition | -0.0083 | 0.2487 | -0.496 | 0.480 | 0.0 | 1129.0 | 0.9735 |
| H-High Marsh | -0.0732 | 0.2170 | -0.499 | 0.353 | -0.3 | 1129.0 | 0.7358 |
| UE-Upland Edge | 0.2727 | 0.3406 | -0.396 | 0.941 | 0.8 | 1131.6 | 0.4236 |
| R2m | R2c |
|---|---|
| 0.129 | 0.56 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 405.6369 | 405.6369 | 1 | 1130.18 | 1.77 | 0.1832 |
| Vegetation_Zone | 42582.9588 | 14194.3196 | 3 | 163.11 | 62.06 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 15343.8677 | 5114.6226 | 3 | 1129.96 | 22.36 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | -1.2837 | 0.2570 | -1.788 | -0.780 | -5.0 | 1130.0 | 0.0000 |
| T-Transition | 1.3771 | 0.2092 | 0.967 | 1.787 | 6.6 | 1129.0 | 0.0000 |
| H-High Marsh | 0.5387 | 0.1825 | 0.181 | 0.897 | 3.0 | 1129.0 | 0.0032 |
| UE-Upland Edge | 0.0000 | 0.2865 | -0.562 | 0.562 | 0.0 | 1131.4 | 1.0000 |
| R2m | R2c |
|---|---|
| 0.524 | 0.773 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 1628.053 | 1628.053 | 1 | 1129.47 | 12.30 | 0.0005 |
| Vegetation_Zone | 4823.244 | 1607.748 | 3 | 129.64 | 12.14 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 1820.403 | 606.801 | 3 | 1129.38 | 4.58 | 0.0034 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | -0.0257 | 0.1955 | -0.409 | 0.358 | -0.1 | 1129.4 | 0.8955 |
| T-Transition | -0.8309 | 0.1591 | -1.143 | -0.519 | -5.2 | 1129.0 | 0.0000 |
| H-High Marsh | -0.3702 | 0.1389 | -0.643 | -0.098 | -2.7 | 1129.0 | 0.0078 |
| UE-Upland Edge | -0.0395 | 0.2181 | -0.467 | 0.388 | -0.2 | 1130.0 | 0.8563 |
| R2m | R2c |
|---|---|
| 0.192 | 0.796 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 11.4839 | 11.4839 | 1 | 1129.57 | 0.08 | 0.7816 |
| Vegetation_Zone | 6866.3541 | 2288.7847 | 3 | 133.87 | 15.32 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 1182.2268 | 394.0756 | 3 | 1129.46 | 2.64 | 0.0484 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | -0.0796 | 0.2077 | -0.487 | 0.328 | -0.4 | 1129.5 | 0.7018 |
| T-Transition | -0.4169 | 0.1691 | -0.749 | -0.085 | -2.5 | 1129.0 | 0.0138 |
| H-High Marsh | 0.0894 | 0.1475 | -0.200 | 0.379 | 0.6 | 1129.0 | 0.5447 |
| UE-Upland Edge | 0.3007 | 0.2316 | -0.154 | 0.755 | 1.3 | 1130.2 | 0.1944 |
| R2m | R2c |
|---|---|
| 0.264 | 0.786 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
This custom metric was calculated using the following formula:
(A-Algae + Spartina alterniflora +
Salicornia depressa + Bare +
Wrack) / Total
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 0.5883 | 0.5883 | 1 | 1130.00 | 23.77 | 0 |
| Vegetation_Zone | 6.7862 | 2.2621 | 3 | 153.81 | 91.39 | 0 |
| Years_sinceStart:Vegetation_Zone | 0.7896 | 0.2632 | 3 | 1129.81 | 10.63 | 0 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.0016 | 0.0027 | -0.004 | 0.007 | 0.6 | 1129.9 | 0.5561 |
| T-Transition | 0.0170 | 0.0022 | 0.013 | 0.021 | 7.8 | 1129.0 | 0.0000 |
| H-High Marsh | 0.0061 | 0.0019 | 0.002 | 0.010 | 3.2 | 1129.0 | 0.0013 |
| UE-Upland Edge | -0.0006 | 0.0030 | -0.006 | 0.005 | -0.2 | 1131.0 | 0.8300 |
| R2m | R2c |
|---|---|
| 0.654 | 0.852 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
This custom metric was calculated using the following formula:
Spartina patens + Distichlis spicata +
Juncus gerardii
The current file contains multiple vegetation zones, and
vegetation zone will be one of the predictors in the statistical
model. Results are presented for each vegetation zone
independently because the marginal effects are of interest to the
project team. However, be careful interpreting zone-wise results if the
interaction term (Years_sinceStart:Vegetation_Zone) is not
significant (p > 0.05).
| Sum Sq | Mean Sq | NumDF | DenDF | F value | Pr(>F) | |
|---|---|---|---|---|---|---|
| Years_sinceStart | 1132.303 | 1132.303 | 1 | 1129.56 | 6.16 | 0.0132 |
| Vegetation_Zone | 17343.311 | 5781.104 | 3 | 133.56 | 31.46 | 0.0000 |
| Years_sinceStart:Vegetation_Zone | 5247.947 | 1749.315 | 3 | 1129.46 | 9.52 | 0.0000 |
| Veg Zone | Trend (per year) | SE | CI lower | CI upper | t | df | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | -0.0346 | 0.2304 | -0.487 | 0.417 | -0.2 | 1129.5 | 0.8807 |
| T-Transition | -1.1477 | 0.1875 | -1.516 | -0.780 | -6.1 | 1129.0 | 0.0000 |
| H-High Marsh | 0.0545 | 0.1636 | -0.266 | 0.375 | 0.3 | 1129.0 | 0.7391 |
| UE-Upland Edge | 0.0717 | 0.2569 | -0.432 | 0.576 | 0.3 | 1130.1 | 0.7801 |
| R2m | R2c |
|---|---|
| 0.421 | 0.833 |
If the interaction between vegetation zone and time was significant (p < 0.05), letters are used to represent groups of slopes that are not significantly different (via pairwise comparisons). If the interaction was not significant, this plot represents the marginal slopes but no letters are used.
Some notes from the function. Kenward-Roger method used to estimate denominator degrees of freedom. Confidence level used: 0.95. p-value adjustment: Tukey. alpha = 0.05.
“If two or more means share the same grouping symbol, then we cannot show them to be different. But we also did not show them to be the same.”
Same plot, but x-axis goes from lowest to highest zone.
These tabs are the multivariate analyses.
In this section, we use multivariate techniques to ordination to visualize and analyze plant community change through plot-level cover data across marsh zones.
The following species/groups were identified by the reserve as important loading factors to display on NMDS outputs.
Sometimes these species do not appear on the plots; usually that is because all data points for that species were 0 or very close to it.
Up to 8 species/groups could be identified specifically in outputs of these multivariate analyses. Reserve choices are:
| Vegetation_Zone | Start | End |
|---|---|---|
| L-Low Marsh | 2010 (20) | 2022 (20) |
| T-Transition | 2010 (32) | 2022 (32) |
| H-High Marsh | 2010 (42) | 2022 (42) |
| UE-Upland Edge | 2010 (16) | 2022 (16) |
| Bare |
| Dead |
| Other Unvegetated |
| Rock |
| Wood |
| Wrack |
| Acer rubrum |
| Achillea millefolium |
| Agalinis maritima |
| Agrostis stolonifera |
| Algae |
| Alnus spp. |
| Amaranthus cannabinus |
| Amelanchier canadensis |
| Ammophila breviligulata |
| Anthoxanthum nitens |
| Apios americana |
| Aquilegia canadensis |
| Arachis spp. |
| Aralia nudicaulis |
| Ascophyllum nodosum |
| Ascophyllum nodosum var. scorpioides |
| Asparagus officinalis |
| Athyrium filix-femina var. angustum |
| Atriplex patula |
| Baccharis halimifolia |
| Berberis thunbergii |
| Betula populifolia |
| Bidens spp. |
| Boehmeria cylindrica |
| Bolboschoenus maritimus |
| Bolboschoenus robustus |
| Calystegia sepium |
| Carex hormathodes |
| Carex paleacea |
| Carex pensylvanica |
| Carex spp. |
| Carex stricta |
| Carya ovata |
| Chelone glabra |
| Cinna arundinacea |
| Cuscuta gronovii |
| Cuscuta spp. |
| Cyperus spp. |
| Distichlis spicata |
| Drosera rotundifolia |
| Elaeagnus umbellata |
| Eleocharis parvula |
| Eleocharis rostellata |
| Eleocharis spp. |
| Elymus spp. |
| Elymus virginicus |
| Epilobium spp. |
| Equisetum fluviatile |
| Euthamia graminifolia |
| Fagus grandifolia |
| Fallopia convolvulus |
| Fallopia japonica var. japonica |
| Festuca rubra |
| Fucus spiralis |
| Fucus spp. |
| Fucus vesiculosus |
| Galium lanceolatum |
| Galium palustre |
| Geranium spp. |
| Gracilaria spp. |
| Hamamelis virginiana |
| Hibiscus moscheutos |
| Hordeum spp. |
| Hypericum perforatum |
| Ilex glabra |
| Ilex verticillata |
| Impatiens capensis |
| Iris spp. |
| Iris versicolor |
| Iva frutescens |
| Juncus articulatus |
| Juncus balticus |
| Juncus gerardii |
| Juncus spp. |
| Juniperus communis |
| Juniperus spp. |
| Juniperus virginiana |
| Lactuca canadensis |
| Lemna minor |
| Lepidium virginicum |
| Lichen |
| Limonium carolinianum |
| Lonicera japonica |
| Lonicera spp. |
| Lycopus virginicus |
| Lyonia ligustrina |
| Lysimachia maritima |
| Lysimachia quadrifolia |
| Lythrum salicaria |
| Lythrum spp. |
| Maianthemum canadense |
| Maianthemum racemosum ssp. racemosum |
| Mentha arvensis |
| Morella pensylvanica |
| Myosotis spp. |
| Myrica gale |
| Myrica spp. |
| Oenothera biennis |
| Onoclea sensibilis |
| Osmunda regalis |
| Osmundastrum cinnamomeum |
| Panicum virgatum |
| Parthenocissus quinquefolia |
| Persicaria sagittata |
| Phalaris arundinacea |
| Phragmites australis |
| Phragmites australis ssp. americanus |
| Picea spp. |
| Pinus rigida |
| Pinus strobus |
| Plantago maritima |
| Plantago major |
| Pluchea odorata |
| Poa nemoralis |
| Polygonum ramosissimum |
| Potentilla anserina |
| Prunus avium |
| Prunus maritima |
| Prunus serotina |
| Prunus virginiana |
| Pseudognaphalium obtusifolium |
| Pteridium aquilinum |
| Puccinellia maritima |
| Pyrus spp. |
| Quercus alba |
| Quercus bicolor |
| Quercus ilicifolia |
| Quercus rubra |
| Quercus spp. |
| Rhamnus cathartica |
| Rhamnus spp. |
| Rhododendron spp. |
| Rosa multiflora |
| Rosa palustris |
| Rosa rugosa |
| Rosa spp. |
| Rubus spp. |
| Rumex crispus |
| Ruppia maritima |
| Salicornia depressa |
| Salicornia maritima |
| Salicornia spp. |
| Salix spp. |
| Sambucus nigra |
| Schoenoplectus americanus |
| Schoenoplectus pungens |
| Schoenoplectus spp. |
| Scirpus atrovirens |
| Scirpus cyperinus |
| Scutellaria lateriflora |
| Setaria spp. |
| Smilax regelii |
| Smilax rotundifolia |
| Smilax spp. |
| Solanum dulcamara |
| Solidago rugosa |
| Solidago sempervirens |
| Solidago spp. |
| Sonchus oleraceus |
| Spartina alterniflora |
| Spartina alterniflora (short) |
| Spartina patens |
| Spartina patens hybrid |
| Spartina pectinata |
| Spartina X caespitosa |
| Spergularia salina |
| Sphagnum spp. |
| Spiraea alba |
| Spiraea alba var. latifolia |
| Spiraea spp. |
| Spiraea tomentosa |
| Suaeda linearis |
| Suaeda maritima |
| Symphyotrichum ericoides |
| Symphyotrichum novi-belgii |
| Symphyotrichum spp. |
| Symphyotrichum subulatum |
| Symphyotrichum tenuifolium |
| Symplocarpus foetidus |
| Teucrium canadense |
| Thalictrum dioicum |
| Thalictrum pubescens |
| Thelypteris noveboracensis |
| Thelypteris palustris |
| Thinopyrum pungens |
| Thinopyrum pycnanthum |
| Toxicodendron radicans |
| Triadenum virginicum |
| Trientalis borealis |
| Triglochin maritima |
| Typha angustifolia |
| Typha latifolia |
| Ulva lactuca |
| Ulva spp. |
| Vaccinium angustifolium |
| Vaccinium corymbosum |
| Vaucheria spp. |
| Viburnum dentatum |
| Vicia cracca |
| Viola cucullata |
| Unknown 1 |
| Unknown 2 |
| Unknown 3 |
H0: Community change (if any) between start and end is consistent across vegetation zones.
The interaction p-value (Vegetation_Zone:Time_group) is
what to look at here:
Time_group to determine whether, across all zones, the
community was different at the end of monitoring than at the
beginning.Permutations have been restricted so that time points are only permuted within a vegetation plot, and both time points for a plot are permuted together across vegetation zones.
If only one vegetation zone is present in the data file, the overall PERMANOVA will be skipped; look in the zone-wise PERMANOVA section below for results.
| Df | SumOfSqs | R2 | F | Pr(>F) | |
|---|---|---|---|---|---|
| Time_group | 1 | 0.9464 | 0.0135 | 4.1105 | 0.002 |
| Vegetation_Zone | 3 | 18.8937 | 0.2701 | 27.3550 | 0.001 |
| Time_group:Vegetation_Zone | 3 | 1.2897 | 0.0184 | 1.8672 | 0.015 |
| Residual | 212 | 48.8083 | 0.6979 | ||
| Total | 219 | 69.9380 | 1.0000 |
H0: No community difference between ‘start’ and ‘end’ within a vegetation zone.
Permutations have been restricted so time points are only permuted within a vegetation plot.
| Vegetation Zone | R2 | p.value | p.value_Bonferonni |
|---|---|---|---|
| L-Low Marsh | 0.1309 | 0.010 | 0.040 |
| T-Transition | 0.0902 | 0.001 | 0.004 |
| H-High Marsh | 0.0137 | 0.284 | 1.000 |
| UE-Upland Edge | 0.0355 | 0.313 | 1.000 |
H0: No difference in dispersion between groups.
This is important to check because one of the assumptions of PERMANOVA is homogeneity of dispersion. Dispersion is the multivariate equivalent of variance. If this assumption is violated, caution should be used in interpreting PERMANOVA results.
The test used here is PERMDISP, implemented with the
betadisper function of the vegan package.
| Df | Sum Sq | Mean Sq | F | N.Perm | Pr(>F) | |
|---|---|---|---|---|---|---|
| Groups | 7 | 3.39 | 0.48 | 19.58 | 999 | 0.001 |
| Residuals | 212 | 5.24 | 0.02 |
If the PERMDISP indicated significant difference in dispersions, you should further investigate the following outputs:
| Group | Mean Distance |
|---|---|
| L-Low Marsh; Start | 0.204 |
| L-Low Marsh; End | 0.333 |
| T-Transition; Start | 0.418 |
| T-Transition; End | 0.269 |
| H-High Marsh; Start | 0.541 |
| H-High Marsh; End | 0.542 |
| UE-Upland Edge; Start | 0.547 |
| UE-Upland Edge; End | 0.501 |
| Vegetation Zone | Start.dispersion | End.dispersion | NumDf | DenDf | F.val | N.Perm | p.val |
|---|---|---|---|---|---|---|---|
| L-Low Marsh | 0.205 | 0.335 | 1 | 38 | 7.3 | 999 | 0.008 |
| T-Transition | 0.418 | 0.266 | 1 | 62 | 9.6 | 999 | 0.003 |
| H-High Marsh | 0.541 | 0.542 | 1 | 82 | 0.0 | 999 | 0.959 |
| UE-Upland Edge | 0.547 | 0.502 | 1 | 30 | 1.3 | 999 | 0.282 |
SIMPER was run if:
The p-values determining the above logic are unadjusted. Due to the exploratory nature of these analyses, we did not adjust p-values for multiple comparisons
SIMPER output explanation:
The top 6 species in output are below.
“average” is the average contribution of that species to the Bray-Curtis distance between the two groups (note, this is not expressed in % and the column does not total to 1); “sd” is the standard deviation of the species’ contribution. “cumulative” is the cumulative % contribution for this species and all those above it in the table. Typically people only report species up to the one that brings “cumulative” over 0.7. “p” is a p-value for that species based on permutation tests. “mean_start” is the mean cover of that species in the starting year(s), and “mean_end” is the mean cover of the species in the last year(s) of monitoring.
| average | sd | cumulative | p | mean_start | mean_end | |
|---|---|---|---|---|---|---|
| Spartina alterniflora | 0.1834 | 0.1198 | 0.4328 | 0.022 | 57.3 | 39.0 |
| Bare | 0.1706 | 0.1245 | 0.8355 | 0.008 | 33.1 | 55.2 |
| Wrack | 0.0217 | 0.0474 | 0.8868 | 0.063 | 4.2 | 0.3 |
| Dead | 0.0138 | 0.0166 | 0.9193 | 0.885 | 1.8 | 2.1 |
| Fucus vesiculosus | 0.0128 | 0.0346 | 0.9497 | 0.264 | 0.3 | 2.4 |
| Spartina patens | 0.0040 | 0.0163 | 0.9591 | 0.504 | 0.8 | 0.0 |
| average | sd | cumulative | p | mean_start | mean_end | |
|---|---|---|---|---|---|---|
| Spartina alterniflora | 0.1711 | 0.1094 | 0.3046 | 0.002 | 34.7 | 57.5 |
| Bare | 0.0975 | 0.0920 | 0.4783 | 0.249 | 16.6 | 22.4 |
| Spartina patens | 0.0869 | 0.0972 | 0.6330 | 0.016 | 16.3 | 5.7 |
| Dead | 0.0679 | 0.1020 | 0.7538 | 0.148 | 12.7 | 5.2 |
| Wrack | 0.0508 | 0.0954 | 0.8443 | 0.028 | 9.6 | 1.5 |
| Distichlis spicata | 0.0337 | 0.0619 | 0.9044 | 0.126 | 4.2 | 3.6 |
| None |
|---|
| SIMPER not run |
| None |
|---|
| SIMPER not run |
In this section, NMDS is performed on data from only the starting and ending years for each vegetation zone. This tab essentially illustrates the PERMANOVA results. For NMDS with all years, see the tab ‘NMDS - all years’.
Non-metric multidimensional scaling is an ordination method that preserves ranked dissimilarities between observations. Exact calculated distances are not preserved in this type of ordination. Points that are closer together on the graphs are more similar than points that are further away, so NMDS is good for seeing groupings and gradients when present. For more information, see the sources referenced below.
This NMDS used Bray-Curtis dissimilarity on the full species matrix (see ‘About’ tab for list of species included), and 3 dimensions.
Final 3-dimensional NMDS stress was 0.1368.
Rules of thumb for interpreting stress, based on the sources below, are:
For more information on NMDS:
Clarke, K. R. (1993). Non-parametric multivariate analyses of changes in community structure. Australian Journal of Ecology, 18(1), Article 1. https://doi.org/10.1111/j.1442-9993.1993.tb00438.x
Clarke, K. R., & Warwick, R. M. (2001). Change in Marine Communities: An Approach to Statistical Analysis and Interpretation, 2nd ed. - Chapter 5 focuses on NMDS.
Zuur, A. F., Ieno, E. N., & Smith, G. M. (2007). Analysing ecological data. Springer. - Chapter 15 for NMDS.
(first two axes only)
The below plots, rather than using arrows for individual species or
vegetation groups, create contours for the specific values of each.
Contours are labeled with % cover values and are fit as a spline-based
surface using vegan::ordisurf().
## Right now, only individual species and not species groups can be used in contour plots. A-Algae is not plotted here.
##
## Right now, only individual species and not species groups can be used in contour plots. B-Brackish is not plotted here.
##
## Right now, only individual species and not species groups can be used in contour plots. F-Freshwater is not plotted here.
##
## Right now, only individual species and not species groups can be used in contour plots. H-Halophyte is not plotted here.
## Right now, only individual species and not species groups can be used in contour plots. U-Upland is not plotted here.
##
## Right now, only individual species and not species groups can be used in contour plots. Unvegetated category is not plotted here.
This 3-d plot is interactive - you can zoom in and rotate the view. Each point represents a single vegetation plot at a single time point (start, open circles; or end, filled circles). Point color represents the plot’s vegetation zone. The red lines and labels represent the coordinates of species or species groups (centroid of comprising species) specified in the Analysis_Specs worksheet of the veg-specs.xlsx file.
No additional loadings specified. If you would like to graph additional environmental factors on the NMDS plot, please specify them in the ‘NMDS additional loadings’ section of the ‘More_Options’ sheet in the veg-specs.xlsx file.
By default, this analysis is not run because it may take more computing power than is available to perform ordination on many years worth of data points.
The all-years NMDS was attempted. If the results are not below, it simply didn’t work with your computer.
All measurements at all veg plots (with 3+ years of data) are represented. Centroids are calculated for each zone x year combination. Plots are zoomable. Two plots are provided: the first uses fixed axis scales, to emphasize where zone centroids are relative to each other in ordination space. The second uses free axis scales, to emphasize within-zone differences between years. There may not be much difference between these visually, depending on the spread of points within each zone. Zooming works differently in each. The loadings plot below applies to both graphs (the entire NMDS).
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